Hm,...maybe "Realms Of The Haunting"?
https://www.gog.com/game/realms_of_the_haunting

Just started playing TimeShift and it's plenty fun. Strange that I haven't heard much about it, was it eclipsed by Crysis that was released the same year?

I second both of these. At least the first Witchaven game, as the second was...well, not so good, in my opinion.

I'll also second Chasm: The Rift and Cybermage.

I'd always heard good things about Wheel of Time, but never played it, so I can't really attest to its worth aside from a curiosity.

I'll also second Shadowcaster, especially the CD ROM version, as it included more multimedia options. It was pretty unique, with shapeshifting powers, built on the Ultima Underworld engine. Played it quite a bit during my teenage years.

As for titles that haven't been mentioned yet, I'm going to throw these ones into the hat.

Operation: Bodycount - In retrospect it was kinda clunky, but it had you running around a big corporate skyscraper, shooting up terrorists with Uzis, Galils, etc.

Fortress of Dr. Radiaki - This was probably also a terrible game, but you were basically hunting a mad scientist who was essentially creating cybernetic samurai operated by brains in jars. Weird game, but I played it quite a bit growing up.

ZPC: I mean, you get to play as basically Jesus, in a uniquely artistic aesthetic that was Killer 7 before Killer 7, blasting away at a post industrial evil empire, to a soundtrack by two of the members of Ministry. If you don't think that's the tightest shit ever, get out my face. (Kidding!) :D

resurrecting this thread becasue it deserves more attention
I found this blog to be a trove for obscure FPS games, some of them quite good!
https://wkduffy.wordpress.com/

Timesplitters for PS2 must be kind of obscure. I had tons of with the level editor in that game.

Kingpin if that counts as obscure enough- not many people have really played it anyway. It came out around the same time as Half Life and I much preferred Kingpin. One of the boss fights is Jesus, what more could you want?

For sure KILLING TIME. That game has it all: weird level design, crappy movement controls, a bizarre story, very bizarre music, evil killer clowns, flying red skulls that shoot fireballs, zombie cooks that throw knifes at you, cockroaches that spit acid, dogs with two heads, unescapeable death traps, a undead mummy that will chase you like Nemesis in Resident Evil 3 and health pickups that damage you.

Is C&C Renegade obscure enough for this thread?
Definitely one of my favorite FPS games.

Tron 2.0 is another one I really loved (not sure if that's obscure enough either though)

I would say Legendary, good idea and story, but full of bugs and unused potential.